quantum-espresso/QEHeat/examples

INSTALLATION OVERVIEW

Before running the examples, you need to be sure that QEHeat is installed. To compile, we suggest the following procedure. As usual in a QuantumEspresso installation, enter the distribution folder and run autoconf :

 > ./configure

Than from the distribution folder:

 >  make all_currents

This will produce the executable all_currents.x, the executable for QEHeat, in the respective src and bin folders.

EXAMPLES

See also ../Doc/INPUT_ALL_CURRENTS.html for a description of the inputs. To run an example, enter in the respective trajectory and execute the script run_example.sh. Modify it if necessary. In general, running a Qeheat calculation just needs the execution of the command: all_currents.x -in input_energycurrent , after the input file has been prepared.

Each example comes with a reference folder where the output files can be compared with the ones produced by a new installation/run. Pseudopotentials can be downloaded from http://www.quantum-simulation.org/potentials/sg15_oncv/ For the examples, the following pseudos were used: H_HSCV_PBE-1.0.upf, O_HSCV_PBE-1.0.upf, O_ONCV_PBE-1.0.upf, Si_ONCV_PBE-1.1.upf , which should be present in the folder pseudo

Example 1 and 2 need a parallel installation to finish in a reasonable time. Example 1 was run in the reference calculation on 4 cores and Example 2 on 12.

Example 3 can be easily run on a single core (serial) installation. Note that Example 3 requires the program cp.x to be installed, for example with make cp from the main distribution folder.

1. example_SiO2_single

Here we compute the energy current and its indivial components for a single snapshot of Silica. For this purpose, one needs the additional namelist in the input file :

&energy_current
    delta_t=   0.500,
    file_output= 'current_hz',
    eta=   0.100,
    n_max=     5,
 /

& IONS
    ion_velocities = 'from_input',

and the CARD ATOMIC_VELOCITIES in the input file must be filled as well with the istantenous atomic velocities. These are the ingredients needed for a basic single snapshot calculation.

The files produced, apart from the standard output, are :

• file_output.dat : this reports the total energy current, the eletronic current and the center of mass velocity for each species. Only file_output.dat needs to be used to evaluate the thermal conductivity coefficient.

• file_output : this reports the total energy current divided in individual components, if a more specific analysis is needed. This file is mainly thought for development purposes.

file_output.dat comes with a header specifying the output units. The same units are used in the more detailed current decomposion given in file_output. See also the description ../Doc/INPUT_ALL_CURRENTS.html

2. example_H2O_trajectory

Here we evaluate the energy current from a previously computed Car-Parrinello (CP) trajectory, which is provided together with the input file. The trajectory provided comes from a 125 water molecule simulation.

We calculate the energy current for every timestep of the trajectory located in ${trajdir}.pos and ${trajdir}.vel (velocities are in CP units in this example). For this purpose we need to insert some additional keywords in the energy_current namelists :

 &energy_current
    delta_t=   0.500,
    file_output= 'current_hz',
    eta=   0.100,
    n_max=     5,
    trajdir='traj'
    first_step=1,
    vel_input_units='CP'
 /

note that the only different keywords with respect to a single snapshot calculations are trajdir and first_step in the energy_current namelist. Still, in the IONS namelist the keyword ion_velocities='from_input' must be set and the ATOMIC_VELOCITIES card must be filled.

The output with the istantenous energy currents is written in the files with names ${file_output} and ${file_output}.dat, as in example 1. The same format of the single snapshot calculation is kept, data from all the snapshots of the trajectory being appended sequentially.

If computational time is an issue, for this example we suggest to insert the flag last_step=xxx in the energy_current namelist, replacing xxx with the desired index step, and than execute the run script. Note that the keywords last_step and first_step refer to the indexes reported in the files ${trajdir}.pos and ${trajdir}.vel and are not sequential indexes. The snapshot in the input file is assigned an index 0. As a concrete example, the combination of first_step=1 and last_step=953008 will skip the snapshot of the input file and evaluate only the first snapshot of the trajectory because 953008 is the first index that appears in the trajectory file.

3. example_small_H2O_trajectory

This example is very similar to the previous one, but a Car-Parrinello trajectory is computed on-the-fly via the cp.x program of the just installed QE distribution. It produces the
trajectory of a single water molecule and therefore the calculation is suited for a serial environment.

This example requires the program cp.x to be installed. If this is not the case, you can enter the distribution folder and run "make cp".

Note that the trajectory produced by cp.x will be probably different due to the stochasticity inherent in the Car-Parrinello molecular dynamics simulation. For exact comparison with a novel installation one can substitute trajdir='reference/traj/cp' and comment in the run_example_water script the call to cp.x. This way the files produced by file_output should be comparable with the reference, up to numerical noise that is always present in the finite difference derivative with non perfectly converged wavefunctions.